Welcome to E-Cell4 in Jupyter Notebook!

E-Cell System is, a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell. E-Cell4 is a free and open-source software licensed under the GNU General Public License version 2. The source code is available on GitHub.

Tutorials

1. Brief Tour of E-Cell4 Simulations local ipynb readthedocs
   • Quick Demo
   • Spatial Simulation and Visualization
2. How to Build a Model local ipynb readthedocs
   • Species
   • ReactionRule
   • NetworkModel
   • Python Utilities to Build a Model
3. How to Setup the Initial Condition local ipynb readthedocs
   • Common APIs of World
   • How to Get Positions of Molecules
   • Lattice-based Coordinate
   • Structure
   • Random Number Generator
4. How to Run a Simulation local ipynb readthedocs
   • How to Setup a Simulator
   • Running Simulation
   • Capsulizing Algorithm into a Factory Class
5. How to Log and Visualize Simulations local ipynb readthedocs
   • Logging Simulations with Observers
   • Visualization of Data Logged
6. How to Solve ODEs with Rate Law Functions local ipynb readthedocs
   • ode.ODEReactionRule
   • ode.ODERatelaw
   • ode.ODENetworkModel
   • References in a Rate Law
   • More about ode
7. Introduction of Rule-based Modeling local ipynb readthedocs
   • Species.count
   • ReactionRule.count and generate
   • NetfreeModel
   • Differences between Species, ReactionRule and NetfreeModel
8. More about 1. Brief Tour of E-Cell4 Simulations local ipynb readthedocs
   • Creating ODEWorld
   • How to Use Real3
   • Creating and Running ODESimulator
   • Switching the Solver
9. Spatial Gillespie Method local ipynb readthedocs
   • Spaces in E-Cell4
   • Spatial Gillespie Method
   • Defining Molecular Diffusion Coefficient
   • Molecular localization
   • Molecular initial location and the reaction
10. Spatiocyte Simulations at Single-Molecule Resolution local ipynb readthedocs
    • Spatiocyte Lattice-based Method
    • The Diffusion Movement of Single Molecule
    • The Diffusion Coefficient and the Second-order Reaction
    • The Structure in the Spatiocyte Method
    • The structure and the reaction

Examples

Here is an extremely simple example with a reversible binding reaction:

More examples are available below:

• Attractors local ipynb readthedocs
  • Rössler attractor
  • Modified Chua chaotic attractor
  • Lorenz system
  • Tamari attractor
  • Moore-Spiegel attractor
• Drosophila Circadian Clock local ipynb readthedocs
• Dual Phosphorylation Cycle local ipynb readthedocs
• Simple EGFR model local ipynb readthedocs
• A Simple Model of the Glycolysis of Human Erythrocytes local ipynb readthedocs
• Hodgkin-Huxley Model, FitzHugh–Nagumo Model local ipynb readthedocs
• Lotka-Volterra 2D local ipynb readthedocs
  • The Original Model in Ordinary Differential Equations
  • The Modified Model Decomposed into Elementary Reactions
  • A Lotka-Volterra-like Model in 2D
• MinDE System with Mesoscopic Simulator local ipynb readthedocs
• MinDE System with Spatiocyte Simulator local ipynb readthedocs
• Simple Equilibrium local ipynb readthedocs
• Tyson1991 local ipynb readthedocs